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Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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Abstract
Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.
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Wang R, Cao Y, Kong F, Hou B, Zhao J, Kang Y, Ye J, Wu H, Zhang H. Developmental regulator RamRsl controls both morphological development and lincomycin biosynthesis in Streptomyces lincolnensis. J Appl Microbiol 2022; 133:400-409. [DOI: doi.org/10.1111/jam.15568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Abstract
Aims
Assessing the role of ramRsl, a gene absent in a lincomycin over-producing strain, in the regulation of morphological development and lincomycin biosynthesis in Streptomyces lincolnensis.
Methods and Results
The gene ramRsl was deleted from the wild-type strain NRRL 2936 and the ΔramR mutant strain was characterized by a slower growth rate and a delayed morphological differentiation compared to the original strain NRRL 2936. Furthermore, the ΔramR produced 2.6-fold more lincomycin than the original strain, and consistently the level of expression of all lincomycin cluster located genes was enhanced at 48 and 96 h in the ΔramR. Complementation of ΔramR with an intact copy of ramRsl restored all wild-type features, whereas the over-expression of ramRsl led to a reduction of 33% of the lincomycin yield. Furthermore, the level of expression of glnR, bldA and SLCG_2919, three of known lincomycin biosynthesis regulators, was lower in the ΔramR than in the original strain at the early stage of fermentation and we demonstrated, using electrophoretic mobility shift assay and XylE reporter assay, that glnR is a novel direct target of RamR.
Conclusions
Altogether, these results indicated that, beyond promoting the morphological development, RamR regulates negatively lincomycin biosynthesis and positively the expression of the nitrogen regulator GlnR.
Significance and Impact of the Study
We demonstrated that RamR plays a negative role in the regulation of lincomycin biosynthesis in S. lincolnensis. Interestingly, the deletion of this gene in other antibiotic-producing Streptomyces strains might also increase their antibiotic-producing abilities.
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Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Yuan Cao
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Fanjing Kong
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
| | - Jiaqi Zhao
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
- Department of Applied Biology East China University of Science and Technology Shanghai China
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4
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Wang R, Cao Y, Kong F, Hou B, Zhao J, Kang Y, Ye J, Wu H, Zhang H. Developmental regulator RamR sl controls both morphological development and lincomycin biosynthesis in Streptomyces lincolnensis. J Appl Microbiol 2022; 133:400-409. [PMID: 35384192 DOI: 10.1111/jam.15568] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
AIMS Assessing the role of ramRsl , a gene absent in a lincomycin over-producing strain, in the regulation of morphological development and lincomycin biosynthesis in S. lincolnensis. METHODS AND RESULTS The gene ramRsl was deleted from the wild type strain NRRL 2936 and the ΔramR mutant strain was characterized by a slower growth rate and a delayed morphological differentiation compared to the original strain NRRL 2936. Furthermore, the ΔramR produced 2.6-fold more lincomycin than the original strain, and consistently the level of expression of all lincomycin cluster located genes was enhanced at 48 h and 96 h in the ΔramR. Complementation of ΔramR with an intact copy of ramRsl restored all wild type features whereas the over-expression of ramRsl led to a reduction of 33% of the lincomycin yield. Furthermore, the level of expression of glnR, bldA, and SLCG_2919, three of known lincomycin biosynthesis regulators, was lower in the ΔramR than in the original strain at the early stage of fermentation and we demonstrated, using EMSA and XylE reporter assay, that glnR is a novel direct target of RamR. CONCLUSIONS Altogether these results indicated that, beyond promoting the morphological development, RamR regulates negatively lincomycin biosynthesis and positively the expression of the nitrogen regulator GlnR. SIGNIFICANCE AND IMPACT OF THE STUDY We demonstrated that RamR plays a negative role in the regulation of lincomycin biosynthesis in S. lincolnensis. Interestingly, the deletion of this gene in other antibiotic producing Streptomyces strains might also increase their antibiotic producing abilities.
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Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuan Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Fanjing Kong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Jiaqi Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, China
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Muok AR, Claessen D, Briegel A. Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria. THE ISME JOURNAL 2021; 15:2591-2600. [PMID: 33723381 PMCID: PMC8397704 DOI: 10.1038/s41396-021-00952-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 01/31/2023]
Abstract
Streptomycetes are sessile bacteria that produce metabolites that impact the behavior of microbial communities. Emerging studies have demonstrated that Streptomyces spores are distributed through various mechanisms, but it remains unclear how spores are transported to their preferred microenvironments, such as plant roots. Here, we show that Streptomyces spores are capable of utilizing the motility machinery of other soil bacteria. Motility assays and microscopy studies reveal that Streptomyces spores are transported to plant tissues by interacting directly with the flagella of both gram-positive and gram-negative bacteria. Genetics experiments demonstrate that this form of motility is facilitated by structural proteins on the spore coat. These results demonstrate that nonmotile bacteria are capable of utilizing the motility machinery of other microbes to complete necessary stages of their lifecycle.
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Affiliation(s)
- Alise R. Muok
- grid.5132.50000 0001 2312 1970Institute for Biology, Leiden University, Leiden, The Netherlands ,grid.5132.50000 0001 2312 1970Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- grid.5132.50000 0001 2312 1970Institute for Biology, Leiden University, Leiden, The Netherlands ,grid.5132.50000 0001 2312 1970Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Ariane Briegel
- grid.5132.50000 0001 2312 1970Institute for Biology, Leiden University, Leiden, The Netherlands ,grid.5132.50000 0001 2312 1970Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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Current Understanding on Adhesion and Biofilm Development in Actinobacteria. Int J Microbiol 2021; 2021:6637438. [PMID: 34122552 PMCID: PMC8166509 DOI: 10.1155/2021/6637438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 05/07/2021] [Indexed: 12/30/2022] Open
Abstract
Biofilm formation and microbial adhesion are two related and complex phenomena. These phenomena are known to play an important role in microbial life and various functions with positive and negative aspects. Actinobacteria have wide distribution in aquatic and terrestrial ecosystems. This phylum is very large and diverse and contains two important genera Streptomyces and Mycobacteria. The genus Streptomyces is the most biotechnologically important, while the genus Mycobacteria contains the pathogenic species of Mycobacteriaceae. According to the literature, the majority of studies carried out on actinomycetes are focused on the detection of new molecules. Despite the well-known diversity and metabolic activities, less attention has been paid to this phylum. Research on adhesion and biofilm formation is not well developed. In the present review, an attempt has been made to review the literature available on the different aspects on biofilm formation and adhesion of Actinobacteria. We focus especially on the genus Streptomyces. Furthermore, a brief overview about the molecules and structures involved in the adhesion phenomenon in the most relevant genus is summarized. We mention the mechanisms of quorum sensing and quorum quenching because of their direct association with biofilm formation.
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Dokouhaki M, Hung A, Kasapis S, Gras SL. Hydrophobins and chaplins: Novel bio-surfactants for food dispersions a review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Beskrovnaya P, Sexton DL, Golmohammadzadeh M, Hashimi A, Tocheva EI. Structural, Metabolic and Evolutionary Comparison of Bacterial Endospore and Exospore Formation. Front Microbiol 2021; 12:630573. [PMID: 33767680 PMCID: PMC7985256 DOI: 10.3389/fmicb.2021.630573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
Sporulation is a specialized developmental program employed by a diverse set of bacteria which culminates in the formation of dormant cells displaying increased resilience to stressors. This represents a major survival strategy for bacteria facing harsh environmental conditions, including nutrient limitation, heat, desiccation, and exposure to antimicrobial compounds. Through dispersal to new environments via biotic or abiotic factors, sporulation provides a means for disseminating genetic material and promotes encounters with preferable environments thus promoting environmental selection. Several types of bacterial sporulation have been characterized, each involving numerous morphological changes regulated and performed by non-homologous pathways. Despite their likely independent evolutionary origins, all known modes of sporulation are typically triggered by limited nutrients and require extensive membrane and peptidoglycan remodeling. While distinct modes of sporulation have been observed in diverse species, two major types are at the forefront of understanding the role of sporulation in human health, and microbial population dynamics and survival. Here, we outline endospore and exospore formation by members of the phyla Firmicutes and Actinobacteria, respectively. Using recent advances in molecular and structural biology, we point to the regulatory, genetic, and morphological differences unique to endo- and exospore formation, discuss shared characteristics that contribute to the enhanced environmental survival of spores and, finally, cover the evolutionary aspects of sporulation that contribute to bacterial species diversification.
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Affiliation(s)
| | | | | | | | - Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, Health Sciences Mall, The University of British Columbia, Vancouver, BC, Canada
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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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10
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Haist J, Neumann SA, Al-Bassam MM, Lindenberg S, Elliot MA, Tschowri N. Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development. Mol Microbiol 2020; 114:808-822. [PMID: 32797697 DOI: 10.1111/mmi.14581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/20/2020] [Indexed: 12/26/2022]
Abstract
The second messenger bis-3,5-cyclic di-guanosine monophosphate (c-di-GMP) determines when Streptomyces initiate sporulation. c-di-GMP signals are integrated into the genetic differentiation network by the regulator BldD and the sigma factor σWhiG . However, functions of the development-specific diguanylate cyclases (DGCs) CdgB and CdgC, and the c-di-GMP phosphodiesterases (PDEs) RmdA and RmdB, are poorly understood. Here, we provide biochemical evidence that the GGDEF-EAL domain protein RmdB from S. venezuelae is a monofunctional PDE that hydrolyzes c-di-GMP to 5'pGpG. Despite having an equivalent GGDEF-EAL domain arrangement, RmdA cleaves c-di-GMP to GMP and exhibits residual DGC activity. We show that an intact EAL motif is crucial for the in vivo function of both enzymes since strains expressing protein variants with an AAA motif instead of EAL are delayed in development, similar to null mutants. Transcriptome analysis of ∆cdgB, ∆cdgC, ∆rmdA, and ∆rmdB strains revealed that the c-di-GMP specified by these enzymes has a global regulatory role, with about 20% of all S. venezuelae genes being differentially expressed in the cdgC mutant. Our data suggest that the major c-di-GMP-controlled targets determining the timing and mode of sporulation are genes involved in cell division and the production of the hydrophobic sheath that covers Streptomyces aerial hyphae and spores.
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Affiliation(s)
- Julian Haist
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sara Alina Neumann
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Sandra Lindenberg
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marie A Elliot
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Natalia Tschowri
- Department of Biology/Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
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Anderl A, Kolmar H, Fuchsbauer HL. The metal-binding properties of the long chaplin from Streptomyces mobaraensis: A bioinformatic and biochemical approach. J Inorg Biochem 2019; 202:110878. [PMID: 31698184 DOI: 10.1016/j.jinorgbio.2019.110878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
Chaplins are amphiphilic proteins coating the surface of aerial hyphae under formation of amyloid-like rodlet layers in streptomycetes. The long chaplin from Streptomyces mobaraensis, Sm-Chp1, harbors extended histidine-rich stretches allowing protein attachment to metal affinity resins. A comprehensive BLASTP search revealed similarity with many putative metal-binding proteins but the deduced sequence motifs were not shared by histidine-rich domains of well-studied proteins. Biochemical analyses showed affinity of Sm-Chp1 for Ni2+, Cu2+ and Zn2+, a binding capacity of 7-8 metal ions, and dissociation constants in a double digit micromolar range. The occurrence of genes for membrane-bound metal transporters and several intra- and extracellular metalloenzymes in the genome of S. mobaraensis suggests that Sm-Chp1 may be a novel type of translocase shifting metals across the rodlet layer from the environment into the cell wall.
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Affiliation(s)
- Anita Anderl
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany; Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiß-Straße 12, 64287 Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany.
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Bacterial Amyloids: Biogenesis and Biomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:113-159. [DOI: 10.1007/978-981-13-9791-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Van Gerven N, Van der Verren SE, Reiter DM, Remaut H. The Role of Functional Amyloids in Bacterial Virulence. J Mol Biol 2018; 430:3657-3684. [PMID: 30009771 PMCID: PMC6173799 DOI: 10.1016/j.jmb.2018.07.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022]
Abstract
Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets. Functional amyloids are widespread in bacteria, pathogenic and non-pathogenic. Bacterial biofilms most commonly function as structural support in the extracellular matrix of biofilms or spore coats, and in cell–cell and cell-surface adherence. The amyloid state can be the sole structured and functional state, or can be facultative, as a secondary state to folded monomeric subunits. Bacterial amyloids can enhance virulence by increasing persistence, cell adherence and invasion, intracellular survival, and pathogen spread by increased environmental survival. Bacterial amyloids may indirectly inflict disease by triggering inflammation, contact phase activation and possibly induce or aggravate human pathological aggregation disorders.
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Affiliation(s)
- Nani Van Gerven
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sander E Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Dirk M Reiter
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
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14
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Dokouhaki M, Hung A, Prime EL, Qiao GG, Day L, Gras SL. pH-Induced interfacial properties of Chaplin E from Streptomyces coelicolor. Colloids Surf B Biointerfaces 2017; 160:589-597. [PMID: 29028607 DOI: 10.1016/j.colsurfb.2017.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/14/2017] [Accepted: 10/03/2017] [Indexed: 10/18/2022]
Abstract
Chaplin E, or Chp E, is a surface active peptide secreted by Streptomyces coelicolor that adopts different structures depending on solution pH but the effect of these structures on the interfacial properties of Chp E is not known. In experiments paired with simulations, Chp E was found to display pH-dependent interfacial assembly and surface activity. At pH 3.0, Chp E formed an ordered non-amyloidal interfacial film with high surface activity; while at pH 10.0, Chp E self-assembled into a heterogeneous film containing randomly arranged fibrils at the interface that was less surface active compared to the film formed at pH 3.0. In simulations at pH 10.0, Chp E molecules showed a higher propensity for dimerization within the solution phase, lower rate of adsorption to the interface and tighter inter-molecular associations at the interface, consistent with the lower surface activity and smaller interfacial area coverage per molecule measured at this pH compared to at pH 3.0. A model is presented for the role of Chp E in the developmental differentiation of Streptomyces coelicolor, where Chp E contributes to changes in surface tension at low pH and the formation of fibrils on the surface of aerial hyphae at high pH. Our data also suggest Chp E could be a promising surface active agent with functional activity that can be controlled by pH.
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Affiliation(s)
- Mina Dokouhaki
- The Melbourne School of Engineering and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC 3001, Australia
| | - Emma L Prime
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia; Polymer Science Group, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Greg G Qiao
- Polymer Science Group, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Li Day
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand
| | - Sally L Gras
- The Melbourne School of Engineering and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia; The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, VIC 3010, Australia.
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15
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Dokouhaki M, Prime EL, Hung A, Qiao GG, Day L, Gras SL. Structure-Dependent Interfacial Properties of Chaplin F from Streptomyces coelicolor. Biomolecules 2017; 7:E68. [PMID: 28925983 PMCID: PMC5618249 DOI: 10.3390/biom7030068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/27/2022] Open
Abstract
Chaplin F (Chp F) is a secreted surface-active peptide involved in the aerial growth of Streptomyces. While Chp E demonstrates a pH-responsive surface activity, the relationship between Chp F structure, function and the effect of solution pH is unknown. Chp F peptides were found to self-assemble into amyloid fibrils at acidic pH (3.0 or the isoelectric point (pI) of 4.2), with ~99% of peptides converted into insoluble fibrils. In contrast, Chp F formed short assemblies containing a mixture of random coil and β-sheet structure at a basic pH of 10.0, where only 40% of the peptides converted to fibrils. The cysteine residues in Chp F did not appear to play a role in fibril assembly. The interfacial properties of Chp F at the air/water interface were altered by the structures adopted at different pH, with Chp F molecules forming a higher surface-active film at pH 10.0 with a lower area per molecule compared to Chp F fibrils at pH 3.0. These data show that the pH responsiveness of Chp F surface activity is the reverse of that observed for Chp E, which could prove useful in potential applications where surface activity is desired over a wide range of solution pH.
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Affiliation(s)
- Mina Dokouhaki
- Department of Chemical Engineering and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Emma L Prime
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
- Polymer Science Group, Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Andrew Hung
- School of Science, RMIT University, Melbourne, VIC 3001, Australia.
| | - Greg G Qiao
- Polymer Science Group, Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Li Day
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand.
| | - Sally L Gras
- Department of Chemical Engineering and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
- The ARC Dairy Innovation Hub, The University of Melbourne, Parkville, VIC 3010, Australia.
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16
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Dragoš A, Kovács ÁT, Claessen D. The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria. Biomolecules 2017; 7:biom7030060. [PMID: 28783117 PMCID: PMC5618241 DOI: 10.3390/biom7030060] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023] Open
Abstract
Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development. Despite this variety of tasks, we know surprisingly little about how their assembly is organized to fulfill all these roles.
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Affiliation(s)
- Anna Dragoš
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Dennis Claessen
- Institute of Biology, Leiden University, 2333BE Leiden, The Netherlands.
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17
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The pH-dependent assembly of Chaplin E from Streptomyces coelicolor. J Struct Biol 2017; 198:82-91. [PMID: 28400129 DOI: 10.1016/j.jsb.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/06/2017] [Accepted: 04/07/2017] [Indexed: 01/01/2023]
Abstract
Chaplin E, is one of five self-assembling peptides secreted by Streptomyces coelicolor that assist aerial growth by lowering the surface tension of water. Although the surface activity of a mixture of chaplin peptides has observed to depend on pH, it is unclear how the solvent environment (i.e. pH) influences the structure, assembly and subsequent functionality of these individual peptides. In this study, the conformation and fibril forming propensity of the Chaplin E peptide was assessed as a function of pH using a combination of experimental measurements and molecular dynamics simulations. At an acidic pH of 3.0, Chaplin E retained a random coil structure, whereas at the isoelectric point of 6.7 or a basic pH of 10.0, Chaplin E rapidly formed amyloid fibrils rich in β-sheet structure with high efficiency (>93%). Molecular dynamics simulations indicate the persistence of greater α-helical content at the N-terminus at high pH; this is likely partly due to the lack of electrostatic repulsion between residues His6 and Lys10. Since fibril formation was observed at high but not at low pH, we propose that the presence of an N-terminal α-helix in the monomeric form of Chaplin E is required for aggregation and conversion to β-amyloid fibrils. The pH sensitivity of Chaplin E peptide structure provides a route to control peptide assembly and may be important for the physiological function of this peptide, as a surface active agent in the transition from vegetative to aerial growth and could assist Streptomyces coelicolor in response to environmental fluctuations in pH.
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18
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Sunde M, Pham CLL, Kwan AH. Molecular Characteristics and Biological Functions of Surface-Active and Surfactant Proteins. Annu Rev Biochem 2017; 86:585-608. [PMID: 28125290 DOI: 10.1146/annurev-biochem-061516-044847] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many critical biological processes take place at hydrophobic:hydrophilic interfaces, and a wide range of organisms produce surface-active proteins and peptides that reduce surface and interfacial tension and mediate growth and development at these boundaries. Microorganisms produce both small lipid-associated peptides and amphipathic proteins that allow growth across water:air boundaries, attachment to surfaces, predation, and improved bioavailability of hydrophobic substrates. Higher-order organisms produce surface-active proteins with a wide variety of functions, including the provision of protective foam environments for vulnerable reproductive stages, evaporative cooling, and gas exchange across airway membranes. In general, the biological functions supported by these diverse polypeptides require them to have an amphipathic nature, and this is achieved by a diverse range of molecular structures, with some proteins undergoing significant conformational change or intermolecular association to generate the structures that are surface active.
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Affiliation(s)
- Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences and Australian Institute for Nanoscale Science and Technology, University of Sydney, NSW 2006, Australia; ,
| | - Chi L L Pham
- Discipline of Pharmacology, School of Medical Sciences and Australian Institute for Nanoscale Science and Technology, University of Sydney, NSW 2006, Australia; ,
| | - Ann H Kwan
- School of Life and Environmental Sciences and Australian Institute for Nanoscale Science and Technology, University of Sydney, NSW 2006, Australia;
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19
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Yin JC, Fei CH, Lo YC, Hsiao YY, Chang JC, Nix JC, Chang YY, Yang LW, Huang IH, Wang S. Structural Insights into Substrate Recognition by Clostridium difficile Sortase. Front Cell Infect Microbiol 2016; 6:160. [PMID: 27921010 PMCID: PMC5118464 DOI: 10.3389/fcimb.2016.00160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/07/2016] [Indexed: 01/07/2023] Open
Abstract
Sortases function as cysteine transpeptidases that catalyze the covalent attachment of virulence-associated surface proteins into the cell wall peptidoglycan in Gram-positive bacteria. The substrate proteins targeted by sortase enzymes have a cell wall sorting signal (CWSS) located at the C-terminus. Up to date, it is still not well understood how sortases with structural resemblance among different classes and diverse species of bacteria achieve substrate specificity. In this study, we focus on elucidating the molecular basis for specific recognition of peptide substrate PPKTG by Clostridium difficile sortase B (Cd-SrtB). Combining structural studies, biochemical assays and molecular dynamics simulations, we have constructed a computational model of Cd-SrtBΔN26-PPKTG complex and have validated the model by site-directed mutagensis studies and fluorescence resonance energy transfer (FRET)-based assay. Furthermore, we have revealed that the fourth amino acid in the N-terminal direction from cleavage site of PPKTG forms specific interaction with Cd-SrtB and plays an essential role in configuring the peptide to allow more efficient substrate-specific cleavage by Cd-SrtB.
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Affiliation(s)
- Jui-Chieh Yin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung UniversityTainan, Taiwan
| | - Chun-Hsien Fei
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung UniversityTainan, Taiwan
| | - Yen-Chen Lo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchu, Taiwan,Bioinformatics Program, Taiwan International Graduate Program, Academia SinicaTaipei, Taiwan
| | - Yu-Yuan Hsiao
- Department of Biological Science and Technology, National Chiao Tung UniversityHsinchu, Taiwan
| | - Jyun-Cyuan Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung UniversityTainan, Taiwan
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchu, Taiwan
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua UniversityHsinchu, Taiwan,Physics Division, National Center for Theoretical SciencesHsinchu, Taiwan,*Correspondence: Lee-Wei Yang
| | - I-Hsiu Huang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung UniversityTainan, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung UniversityTainan, Taiwan,I-Hsiu Huang
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung UniversityTainan, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung UniversityTainan, Taiwan,Shuying Wang
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20
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High-resolution imaging of the microbial cell surface. J Microbiol 2016; 54:703-708. [PMID: 27796933 DOI: 10.1007/s12275-016-6348-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 10/20/2022]
Abstract
Microorganisms, or microbes, can function as threatening pathogens that cause disease in humans, animals, and plants; however, they also act as litter decomposers in natural ecosystems. As the outermost barrier and interface with the environment, the microbial cell surface is crucial for cell-to-cell communication and is a potential target of chemotherapeutic agents. Surface ultrastructures of microbial cells have typically been observed using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Owing to its characteristics of low-temperature specimen preparation and superb resolution (down to 1 nm), cryo-field emission SEM has revealed paired rodlets, referred to as hydrophobins, on the cell walls of bacteria and fungi. Recent technological advances in AFM have enabled high-speed live cell imaging in liquid at the nanoscale level, leading to clear visualization of cell-drug interactions. Platinum-carbon replicas from freeze-fractured fungal spores have been observed using transmission electron microscopy, revealing hydrophobins with varying dimensions. In addition, AFM has been used to resolve bacteriophages in their free state and during infection of bacterial cells. Various microscopy techniques with enhanced spatial resolution, imaging speed, and versatile specimen preparation are being used to document cellular structures and events, thus addressing unanswered biological questions.
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21
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Schor M, Reid JL, MacPhee CE, Stanley-Wall NR. The Diverse Structures and Functions of Surfactant Proteins. Trends Biochem Sci 2016; 41:610-620. [PMID: 27242193 PMCID: PMC4929970 DOI: 10.1016/j.tibs.2016.04.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/25/2016] [Accepted: 04/29/2016] [Indexed: 01/26/2023]
Abstract
Surface tension at liquid–air interfaces is a major barrier that needs to be surmounted by a wide range of organisms; surfactant and interfacially active proteins have evolved for this purpose. Although these proteins are essential for a variety of biological processes, our understanding of how they elicit their function has been limited. However, with the recent determination of high-resolution 3D structures of several examples, we have gained insight into the distinct shapes and mechanisms that have evolved to confer interfacial activity. It is now a matter of harnessing this information, and these systems, for biotechnological purposes. Interfacially active proteins fulfill a wide range of biological functions in organisms ranging from bacteria and fungi to mammals. Their physicochemical properties make interfacially active proteins attractive for biotechnological applications; for example, as coatings on nanodevices or medical implants and as emulsifiers in food and personal-care products. High-resolution 3D structures show that the mechanisms by which interfacially active proteins achieve their function are highly diverse.
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Affiliation(s)
- Marieke Schor
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Jack L Reid
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Cait E MacPhee
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
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22
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OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons. mSystems 2016; 1:mSystems00014-16. [PMID: 27822533 PMCID: PMC5069765 DOI: 10.1128/msystems.00014-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/29/2016] [Indexed: 11/20/2022] Open
Abstract
Dormancy is a state of growth cessation that allows bacteria to escape the host defense system and antibiotic challenge. Understanding the mechanisms that control dormancy is of key importance for the treatment of latent infections, such as those from Mycobacterium tuberculosis. In mycobacteria, dormancy is controlled by the response regulator DevR, which responds to conditions of hypoxia. Here, we show that OsdR of Streptomyces coelicolor recognizes the same regulatory element and controls a regulon that consists of genes involved in the control of stress and development. Only the core regulon in the direct vicinity of dosR and osdR is conserved between M. tuberculosis and S. coelicolor, respectively. Thus, we show how the system has diverged from allowing escape from the host defense system by mycobacteria to the control of sporulation by complex multicellular streptomycetes. This provides novel insights into how bacterial growth and development are coordinated with the environmental conditions. Two-component regulatory systems allow bacteria to respond adequately to changes in their environment. In response to a given stimulus, a sensory kinase activates its cognate response regulator via reversible phosphorylation. The response regulator DevR activates a state of dormancy under hypoxia in Mycobacterium tuberculosis, allowing this pathogen to escape the host defense system. Here, we show that OsdR (SCO0204) of the soil bacterium Streptomyces coelicolor is a functional orthologue of DevR. OsdR, when activated by the sensory kinase OsdK (SCO0203), binds upstream of the DevR-controlled dormancy genes devR, hspX, and Rv3134c of M. tuberculosis. In silico analysis of the S. coelicolor genome combined with in vitro DNA binding studies identified many binding sites in the genomic region around osdR itself and upstream of stress-related genes. This binding correlated well with transcriptomic responses, with deregulation of developmental genes and genes related to stress and hypoxia in the osdR mutant. A peak in osdR transcription in the wild-type strain at the onset of aerial growth correlated with major changes in global gene expression. Taken together, our data reveal the existence of a dormancy-related regulon in streptomycetes which plays an important role in the transcriptional control of stress- and development-related genes. IMPORTANCE Dormancy is a state of growth cessation that allows bacteria to escape the host defense system and antibiotic challenge. Understanding the mechanisms that control dormancy is of key importance for the treatment of latent infections, such as those from Mycobacterium tuberculosis. In mycobacteria, dormancy is controlled by the response regulator DevR, which responds to conditions of hypoxia. Here, we show that OsdR of Streptomyces coelicolor recognizes the same regulatory element and controls a regulon that consists of genes involved in the control of stress and development. Only the core regulon in the direct vicinity of dosR and osdR is conserved between M. tuberculosis and S. coelicolor, respectively. Thus, we show how the system has diverged from allowing escape from the host defense system by mycobacteria to the control of sporulation by complex multicellular streptomycetes. This provides novel insights into how bacterial growth and development are coordinated with the environmental conditions.
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23
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Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1-43. [PMID: 26609051 PMCID: PMC4711186 DOI: 10.1128/mmbr.00019-15] [Citation(s) in RCA: 936] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
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Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
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24
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c-di-GMP signalling and the regulation of developmental transitions in streptomycetes. Nat Rev Microbiol 2015; 13:749-60. [PMID: 26499894 DOI: 10.1038/nrmicro3546] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complex life cycle of streptomycetes involves two distinct filamentous cell forms: the growing (or vegetative) hyphae and the reproductive (or aerial) hyphae, which differentiate into long chains of spores. Until recently, little was known about the signalling pathways that regulate the developmental transitions leading to sporulation. In this Review, we discuss important new insights into these pathways that have led to the emergence of a coherent regulatory network, focusing on the erection of aerial hyphae and the synchronous cell division event that produces dozens of unigenomic spores. In particular, we highlight the role of cyclic di-GMP (c-di-GMP) in controlling the initiation of development, and the role of the master regulator BldD in mediating c-di-GMP signalling.
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25
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Abstract
Amyloids are insoluble fibrillar protein deposits with an underlying cross-β structure initially discovered in the context of human diseases. However, it is now clear that the same fibrillar structure is used by many organisms, from bacteria to humans, in order to achieve a diverse range of biological functions. These functions include structure and protection (e.g. curli and chorion proteins, and insect and spider silk proteins), aiding interface transitions and cell-cell recognition (e.g. chaplins, rodlins and hydrophobins), protein control and storage (e.g. Microcin E492, modulins and PMEL), and epigenetic inheritance and memory [e.g. Sup35, Ure2p, HET-s and CPEB (cytoplasmic polyadenylation element-binding protein)]. As more examples of functional amyloid come to light, the list of roles associated with functional amyloids has continued to expand. More recently, amyloids have also been implicated in signal transduction [e.g. RIP1/RIP3 (receptor-interacting protein)] and perhaps in host defence [e.g. aDrs (anionic dermaseptin) peptide]. The present chapter discusses in detail functional amyloids that are used in Nature by micro-organisms, non-mammalian animals and mammals, including the biological roles that they play, their molecular composition and how they assemble, as well as the coping strategies that organisms have evolved to avoid the potential toxicity of functional amyloid.
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26
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Caro-Astorga J, Pérez-García A, de Vicente A, Romero D. A genomic region involved in the formation of adhesin fibers in Bacillus cereus biofilms. Front Microbiol 2015; 5:745. [PMID: 25628606 PMCID: PMC4292775 DOI: 10.3389/fmicb.2014.00745] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 12/09/2014] [Indexed: 01/09/2023] Open
Abstract
Bacillus cereus is a bacterial pathogen that is responsible for many recurrent disease outbreaks due to food contamination. Spores and biofilms are considered the most important reservoirs of B. cereus in contaminated fresh vegetables and fruits. Biofilms are bacterial communities that are difficult to eradicate from biotic and abiotic surfaces because of their stable and extremely strong extracellular matrix. These extracellular matrixes contain exopolysaccharides, proteins, extracellular DNA, and other minor components. Although B. cereus can form biofilms, the bacterial features governing assembly of the protective extracellular matrix are not known. Using the well-studied bacterium B. subtilis as a model, we identified two genomic loci in B. cereus, which encodes two orthologs of the amyloid-like protein TasA of B. subtilis and a SipW signal peptidase. Deletion of this genomic region in B. cereus inhibited biofilm assembly; notably, mutation of the putative signal peptidase SipW caused the same phenotype. However, mutations in tasA or calY did not completely prevent biofilm formation; strains that were mutated for either of these genes formed phenotypically different surface attached biofilms. Electron microscopy studies revealed that TasA polymerizes to form long and abundant fibers on cell surfaces, whereas CalY does not aggregate similarly. Heterologous expression of this amyloid-like cassette in a B. subtilis strain lacking the factors required for the assembly of TasA amyloid-like fibers revealed (i) the involvement of this B. cereus genomic region in formation of the air-liquid interphase pellicles and (ii) the intrinsic ability of TasA to form fibers similar to the amyloid-like fibers produced by its B. subtilis ortholog.
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Affiliation(s)
- Joaquín Caro-Astorga
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Universidad de Málaga Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Universidad de Málaga Málaga, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Universidad de Málaga Málaga, Spain
| | - Diego Romero
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Universidad de Málaga Málaga, Spain
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27
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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28
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Petrus MLC, Claessen D. Pivotal roles for Streptomyces cell surface polymers in morphological differentiation, attachment and mycelial architecture. Antonie van Leeuwenhoek 2014; 106:127-39. [PMID: 24682579 DOI: 10.1007/s10482-014-0157-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/12/2014] [Indexed: 01/07/2023]
Abstract
Cells that are part of a multicellular structure are typically embedded in an extracellular matrix, which is produced by the community members. These matrices, the composition of which is highly diverse between different species, are typically composed of large amounts of extracellular polymeric substances, including polysaccharides, proteins, and nucleic acids. The functions of all these matrices are diverse: they provide protection, mechanical stability, mediate adhesion to surfaces, regulate motility, and form a cohesive network in which cells are transiently immobilized. In this review we discuss the role of matrix components produced by streptomycetes during growth, development and attachment. Compared to other bacteria it appears that streptomycetes can form morphologically and functionally distinct matrices using a core set of building blocks.
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Affiliation(s)
- Marloes L C Petrus
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Sylviusweg 72, 2300 RA, Leiden, The Netherlands
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29
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Functional analysis of the accessory protein TapA in Bacillus subtilis amyloid fiber assembly. J Bacteriol 2014; 196:1505-13. [PMID: 24488317 DOI: 10.1128/jb.01363-13] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis biofilm formation relies on the assembly of a fibrous scaffold formed by the protein TasA. TasA polymerizes into highly stable fibers with biochemical and morphological features of functional amyloids. Previously, we showed that assembly of TasA fibers requires the auxiliary protein TapA. In this study, we investigated the roles of TapA sequences from the C-terminal and N-terminal ends and TapA cysteine residues in its ability to promote the assembly of TasA amyloid-like fibers. We found that the cysteine residues are not essential for the formation of TasA fibers, as their replacement by alanine residues resulted in only minor defects in biofilm formation. Mutating sequences in the C-terminal half had no effect on biofilm formation. However, we identified a sequence of 8 amino acids in the N terminus that is key for TasA fiber formation. Strains expressing TapA lacking these 8 residues were completely defective in biofilm formation. In addition, this TapA mutant protein exhibited a dominant negative effect on TasA fiber formation. Even in the presence of wild-type TapA, the mutant protein inhibited fiber assembly in vitro and delayed biofilm formation in vivo. We propose that this 8-residue sequence is crucial for the formation of amyloid-like fibers on the cell surface, perhaps by mediating the interaction between TapA or TapA and TasA molecules.
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30
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Chaplins of Streptomyces coelicolor self-assemble into two distinct functional amyloids. J Struct Biol 2013; 184:301-9. [DOI: 10.1016/j.jsb.2013.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/23/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022]
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Abstract
Bacterial biofilms are ubiquitous in nature, and their resilience is derived in part from a complex extracellular matrix that can be tailored to meet environmental demands. Although common developmental stages leading to biofilm formation have been described, how the extracellular components are organized to allow three-dimensional biofilm development is not well understood. Here we show that uropathogenic Escherichia coli (UPEC) strains produce a biofilm with a highly ordered and complex extracellular matrix (ECM). We used electron microscopy (EM) techniques to image floating biofilms (pellicles) formed by UPEC. EM revealed intricately constructed substructures within the ECM that encase individual, spatially segregated bacteria with a distinctive morphology. Mutational and biochemical analyses of these biofilms confirmed curli as a major matrix component and revealed important roles for cellulose, flagella, and type 1 pili in pellicle integrity and ECM infrastructure. Collectively, the findings of this study elucidated that UPEC pellicles have a highly organized ultrastructure that varies spatially across the multicellular community. Bacteria can form biofilms in diverse niches, including abiotic surfaces, living cells, and at the air-liquid interface of liquid media. Encasing these cellular communities is a self-produced extracellular matrix (ECM) that can be composed of proteins, polysaccharides, and nucleic acids. The ECM protects biofilm bacteria from environmental insults and also makes the dissolution of biofilms very challenging. As a result, formation of biofilms within humans (during infection) or on industrial material (such as water pipes) has detrimental and costly effects. In order to combat bacterial biofilms, a better understanding of components required for biofilm formation and the ECM is required. This study defined the ECM composition and architecture of floating pellicle biofilms formed by Escherichia coli.
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Abstract
Many bacteria produce protein fibrils that are structurally analogous to those associated with protein misfolding diseases such as Alzheimer's disease. However, unlike fibrils associated with disease, bacterial amyloids have beneficial functions including conferring stability to biofilms, regulating development or imparting virulence. In the present review, we consider what makes amyloid fibrils so suitable for these roles and discuss recent developments in the study of bacterial amyloids, in particular the chaplins from Streptomyces coelicolor. We also consider the broader impact of the study of bacterial amyloids on our understanding of infection and disease and on developments in nanotechnology.
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DePas WH, Chapman MR. Microbial manipulation of the amyloid fold. Res Microbiol 2012; 163:592-606. [PMID: 23108148 PMCID: PMC3532741 DOI: 10.1016/j.resmic.2012.10.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/09/2012] [Indexed: 12/19/2022]
Abstract
Microbial biofilms are encased in a protein, DNA, and polysaccharide matrix that protects the community, promotes interactions with the environment, and helps cells adhere together. The protein component of these matrices is often a remarkably stable, β-sheet-rich polymer called amyloid. Amyloids form ordered, self-templating fibers that are highly aggregative, making them a valuable biofilm component. Some eukaryotic proteins inappropriately adopt the amyloid fold, and these misfolded protein aggregates disrupt normal cellular proteostasis, which can cause significant cytotoxicity. Indeed, until recently amyloids were considered solely the result of protein misfolding. However, research over the past decade has revealed how various organisms have capitalized on the amyloid fold by developing sophisticated biogenesis pathways that coordinate gene expression, protein folding, and secretion so that amyloid-related toxicities are minimized. How microbes manipulate amyloids, by augmenting their advantageous properties and by reducing their undesirable properties, will be the subject of this review.
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Affiliation(s)
- William H. DePas
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA
| | - Matthew R. Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan LSA, 830 North University Ave., Ann Arbor, MI, 48109, USA
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Sanssouci É, Lerat S, Daigle F, Grondin G, Shareck F, Beaulieu C. Deletion of TerD-domain-encoding genes: effect on Streptomyces coelicolor development. Can J Microbiol 2012; 58:1221-9. [PMID: 23072443 DOI: 10.1139/w2012-101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
TerD-domain-encoding genes (tdd genes) are highly represented in the Streptomyces coelicolor genome. One of these, the tdd8 gene, was recently shown to have a crucial influence on growth, differentiation, and spore development of this filamentous bacterium. The investigation of the potential role of tdd genes has been extended here to tdd7 (SCO2367) and tdd13 (SCO4277). Both genes are highly expressed in bacteria grown in liquid-rich medium (tryptic soy broth). However, the deletion of these genes in S. coelicolor showed contrasting effects regarding developmental patterns, sporulation, and antibiotic production. Deletion of the tdd7 gene induced a reduction of growth in liquid medium, wrinkling of the mycelium on solid medium, and poor spore and actinorhodin production. On the other hand, deletion of the tdd13 gene did not significantly affect growth in liquid medium but induced a small colony phenotype on solid medium with abundant sporulation and overproduction of undecylprodigiosin. Although their exact functions remain undefined, the present data suggest a major involvement of TerD proteins in the proper development of S. coelicolor.
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Affiliation(s)
- Édith Sanssouci
- Centre d'Étude et de Valorisation de la Diversité Microbienne, Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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Bibb MJ, Domonkos A, Chandra G, Buttner MJ. Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σ(BldN) and a cognate anti-sigma factor, RsbN. Mol Microbiol 2012; 84:1033-49. [PMID: 22582857 DOI: 10.1111/j.1365-2958.2012.08070.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chaplin and rodlin proteins together constitute the major components of the hydrophobic sheath that coats the aerial hyphae and spores in Streptomyces, and mutants lacking the chaplins are unable to erect aerial hyphae and differentiate on minimal media. We have gained insight into the developmental regulation of the chaplin (chp) and rodlin (rdl) genes by exploiting a new model species, Streptomyces venezuelae, which sporulates in liquid culture. Using microarrays, the chaplin and rodlin genes were found to be highly induced during submerged sporulation in a bldN-dependent manner. Using σ(BldN) ChIP-chip, we show that this dependence arises because the chaplin and rodlin genes are direct biochemical targets of σ(BldN) . sven3186 (here named rsbN for regulator of sigma BldN), the gene lying immediately downstream of bldN, was also identified as a target of σ(BldN) . Disruption of rsbN causes precocious sporulation and biochemical experiments demonstrate that RsbN functions as a σ(BldN) -specific anti-sigma factor.
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Affiliation(s)
- Maureen J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
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36
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Duong A, Capstick DS, Di Berardo C, Findlay KC, Hesketh A, Hong HJ, Elliot MA. Aerial development in Streptomyces coelicolor requires sortase activity. Mol Microbiol 2012; 83:992-1005. [PMID: 22296345 DOI: 10.1111/j.1365-2958.2012.07983.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Streptomyces coelicolor is a multicellular bacterium whose life cycle encompasses three differentiated states: vegetative hyphae, aerial hyphae and spores. Among the factors required for aerial development are the 'chaplins', a family of eight secreted proteins that coat the surface of aerial hyphae. Three chaplins (the 'long' chaplins, ChpA, B and C) possess an LAXTG-containing C-terminal sorting signal and are predicted sortase substrates. The five remaining 'short' chaplins are presumed to be associated with the cell surface through interactions with the long chaplins. We show here that two sortase enzymes, SrtE1 and SrtE2, cleave LAXTG-containing peptides at two distinct positions in vitro, and are required for cell wall anchoring of ChpC in vivo. srtE1/E2 double mutants are delayed in aerial hyphae formation, do not sporulate and fail to display all short chaplins on their aerial surfaces. Surprisingly, these mutant characteristics were not shared by a long chaplin mutant, which exhibited only modest delays in aerial development, leading us to revise the current model of chaplin-mediated aerial development. The sortase mutant phenotype, instead, appears to stem from an inability to transcribe aerial hyphae-specific genes, whose products have diverse functions. This suggests that sortase activity triggers an important, and previously unknown, developmental checkpoint.
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Affiliation(s)
- Andrew Duong
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
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McCormick JR, Flärdh K. Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 2012; 36:206-31. [PMID: 22092088 PMCID: PMC3285474 DOI: 10.1111/j.1574-6976.2011.00317.x] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 10/29/2011] [Accepted: 10/30/2011] [Indexed: 12/16/2022] Open
Abstract
Streptomyces coelicolor is the genetically best characterized species of a populous genus belonging to the gram-positive Actinobacteria. Streptomycetes are filamentous soil organisms, well known for the production of a plethora of biologically active secondary metabolic compounds. The Streptomyces developmental life cycle is uniquely complex and involves coordinated multicellular development with both physiological and morphological differentiation of several cell types, culminating in the production of secondary metabolites and dispersal of mature spores. This review presents a current appreciation of the signaling mechanisms used to orchestrate the decision to undergo morphological differentiation, and the regulators and regulatory networks that direct the intriguing development of multigenomic hyphae first to form specialized aerial hyphae and then to convert them into chains of dormant spores. This current view of S. coelicolor development is destined for rapid evolution as data from '-omics' studies shed light on gene regulatory networks, new genetic screens identify hitherto unknown players, and the resolution of our insights into the underlying cell biological processes steadily improve.
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Affiliation(s)
| | - Klas Flärdh
- Department of Biology, Lund University, Lund, Sweden
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Dual amyloid domains promote differential functioning of the chaplin proteins during Streptomyces aerial morphogenesis. Proc Natl Acad Sci U S A 2011; 108:9821-6. [PMID: 21628577 DOI: 10.1073/pnas.1018715108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The chaplin proteins are functional amyloids found in the filamentous Streptomyces bacteria. These secreted proteins are required for the aerial development of Streptomyces coelicolor, and contribute to an intricate rodlet ultrastructure that decorates the surfaces of aerial hyphae and spores. S. coelicolor encodes eight chaplin proteins. Previous studies have revealed that only three of these proteins (ChpC, ChpE, and ChpH) are necessary for promoting aerial development, and of these three, ChpH is the primary developmental determinant. Here, we show that the model chaplin, ChpH, contains two amyloidogenic domains: one in the N terminus and one in the C terminus of the mature protein. These domains have different polymerization properties as determined using fluorescence spectroscopy, secondary structure analyses, and electron microscopy. We coupled these in vitro assays with in vivo genetic studies to probe the connection between ChpH amyloidogenesis and its biological function. Using mutational analyses, we demonstrated that both N- and C-terminal amyloid domains of ChpH were required for promoting aerial hypha formation, while the N-terminal domain was dispensable for assembly of the rodlet ultrastructure. These results suggest that there is a functional differentiation of the dual amyloid domains in the chaplin proteins.
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Sawyer EB, Claessen D, Haas M, Hurgobin B, Gras SL. The assembly of individual chaplin peptides from Streptomyces coelicolor into functional amyloid fibrils. PLoS One 2011; 6:e18839. [PMID: 21526199 PMCID: PMC3079736 DOI: 10.1371/journal.pone.0018839] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 03/21/2011] [Indexed: 02/07/2023] Open
Abstract
The self-association of proteins into amyloid fibrils offers an alternative to the natively folded state of many polypeptides. Although commonly associated with disease, amyloid fibrils represent the natural functional state of some proteins, such as the chaplins from the soil-dwelling bacterium Streptomyces coelicolor, which coat the aerial mycelium and spores rendering them hydrophobic. We have undertaken a biophysical characterisation of the five short chaplin peptides ChpD-H to probe the mechanism by which these peptides self-assemble in solution to form fibrils. Each of the five chaplin peptides produced synthetically or isolated from the cell wall is individually surface-active and capable of forming fibrils under a range of solution conditions in vitro. These fibrils contain a highly similar cross-β core structure and a secondary structure that resembles fibrils formed in vivo on the spore and mycelium surface. They can also restore the growth of aerial hyphae to a chaplin mutant strain. We show that cysteine residues are not required for fibril formation in vitro and propose a role for the cysteine residues conserved in four of the five short chaplin peptides.
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Affiliation(s)
- Elizabeth B. Sawyer
- Department of Chemical and Biomolecular Engineering and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Dennis Claessen
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Maria Haas
- Department of Chemical and Biomolecular Engineering and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Bhavna Hurgobin
- Department of Chemical and Biomolecular Engineering and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Sally L. Gras
- Department of Chemical and Biomolecular Engineering and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
- * E-mail:
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Fowler-Goldsworthy K, Gust B, Mouz S, Chandra G, Findlay KC, Chater KF. The actinobacteria-specific gene wblA controls major developmental transitions in Streptomyces coelicolor A3(2). MICROBIOLOGY-SGM 2011; 157:1312-1328. [PMID: 21330440 DOI: 10.1099/mic.0.047555-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Streptomyces coelicolor A3(2) sporulation gene whiB is the paradigm of a family of genes (wbl, whiB-like) that are confined to actinobacteria. The chromosome of S. coelicolor contains 11 wbl genes, among which five are conserved in many actinobacteria: whiB itself; whiD, a sporulation gene; wblC, which is required for multi-drug resistance; and wblA and wblE, whose roles had previously been little studied. We succeeded in disrupting wblA and the six non-conserved genes, but could not disrupt wblE. Although mutations in the six non-conserved wbl genes (including some multiple wbl mutants) produced no readily detectable phenotype, mutations in wblA had novel and complex effects. The aerial mycelium of wblA mutants was coloured red, because of the ectopic presence of pigmented antibiotics (actinorhodin and undecylprodigiosin) normally confined to lower parts of wild-type colonies, and consisted almost entirely of non-sporulating, thin, straight filaments, often bundled together in a fibrillar matrix. Rare spore chains were also formed, which exhibited wild-type properties but were genetically still wblA mutants. A wblA mutant achieved higher biomass than the wild-type. Microarray analysis indicated major transcriptional changes in a wblA mutant: using a relatively stringent cut-off, 183 genes were overexpressed, including genes for assimilative primary metabolism and actinorhodin biosynthesis, and 103 were underexpressed, including genes associated with stages of aerial hyphal growth. We suggest that WblA is important in both the slow-down of biomass accumulation and the change from aerial hyphal initial cells to the subapical stem and apical compartments that precede sporulation; and that the mutant aerial mycelium consists of recapitulated defective aerial hyphal initial cells.
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Affiliation(s)
- Kay Fowler-Goldsworthy
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Bertolt Gust
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Sébastien Mouz
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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41
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King GM. Enhancing soil carbon storage for carbon remediation: potential contributions and constraints by microbes. Trends Microbiol 2011; 19:75-84. [DOI: 10.1016/j.tim.2010.11.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 11/10/2010] [Accepted: 11/18/2010] [Indexed: 01/30/2023]
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42
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Flärdh K. Cell polarity and the control of apical growth in Streptomyces. Curr Opin Microbiol 2010; 13:758-65. [DOI: 10.1016/j.mib.2010.10.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 01/10/2023]
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43
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Analysis of developmental gene conservation in the Actinomycetales using DNA/DNA microarray comparisons. Antonie van Leeuwenhoek 2010; 99:159-77. [DOI: 10.1007/s10482-010-9473-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 06/11/2010] [Indexed: 01/21/2023]
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44
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Thompson BJ, Widdick DA, Hicks MG, Chandra G, Sutcliffe IC, Palmer T, Hutchings MI. Investigating lipoprotein biogenesis and function in the model Gram-positive bacterium Streptomyces coelicolor. Mol Microbiol 2010; 77:943-57. [PMID: 20572939 DOI: 10.1111/j.1365-2958.2010.07261.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipoproteins are a distinct class of bacterial membrane proteins that are translocated across the cytoplasmic membrane primarily by the Sec general secretory pathway and then lipidated on a conserved cysteine by the enzyme lipoprotein diacylglycerol transferase (Lgt). The signal peptide is cleaved by lipoprotein signal peptidase (Lsp) to leave the lipid-modified cysteine at the N-terminus of the mature lipoprotein. In all Gram-positive bacteria tested to date this pathway is non-essential and the lipid attaches the protein to the outer leaflet of the cytoplasmic membrane. Here we identify lipoproteins in the model Gram-positive bacterium Streptomyces coelicolor using bioinformatics coupled with proteomic and downstream analysis. We report that Streptomyces species translocate large numbers of lipoproteins out via the Tat (twin arginine translocase) pathway and we present evidence that lipoprotein biogenesis might be an essential pathway in S. coelicolor. This is the first analysis of lipoproteins and lipoprotein biogenesis in Streptomyces and provides the first evidence that lipoprotein biogenesis could be essential in a Gram-positive bacterium. This report also provides the first experimental evidence that Tat plays a major role in the translocation of lipoproteins in a specific bacterium.
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Affiliation(s)
- Benjamin J Thompson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - David A Widdick
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew G Hicks
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Govind Chandra
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Iain C Sutcliffe
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tracy Palmer
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.School of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK.School of Medicine, Health Policy and Practice, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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45
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Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H. The complex extracellular biology ofStreptomyces. FEMS Microbiol Rev 2010; 34:171-98. [DOI: 10.1111/j.1574-6976.2009.00206.x] [Citation(s) in RCA: 336] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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46
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The Rhodococcal Cell Envelope: Composition, Organisation and Biosynthesis. BIOLOGY OF RHODOCOCCUS 2010. [DOI: 10.1007/978-3-642-12937-7_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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47
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de Jong W, Wösten HAB, Dijkhuizen L, Claessen D. Attachment of Streptomyces coelicolor is mediated by amyloidal fimbriae that are anchored to the cell surface via cellulose. Mol Microbiol 2009; 73:1128-40. [PMID: 19682261 DOI: 10.1111/j.1365-2958.2009.06838.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The chaplin proteins ChpA-H enable the filamentous bacterium Streptomyces coelicolor to form reproductive aerial structures by assembling into surface-active amyloid-like fibrils. We here demonstrate that chaplins also mediate attachment of S. coelicolor to surfaces. Attachment coincides with the formation of fimbriae, which are connected to the cell surface via spike-shaped protrusions. Mass spectrometry, electron microscopy and Congo red treatment showed that these fimbriae are composed of bundled amyloid fibrils of chaplins. Attachment and fimbriae formation were abolished in a strain in which the chaplin genes chpA-H were inactivated. Instead, very thin fibrils emerged from the spike-shaped protrusions in this mutant. These fibrils were susceptible to cellulase treatment. This enzymatic treatment also released wild-type fimbriae from the cell surface, thereby abolishing attachment. The reduced attachment of a strain in which the gene of a predicted cellulose synthase was inactivated also indicates a role of cellulose in surface attachment. We propose that the mechanism of attachment via cellulose-anchored amyloidal fimbriae is widespread in bacteria and may function in initiation of infection and in formation of biofilms.
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Affiliation(s)
- Wouter de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Microbiology, University of Groningen, Haren, The Netherlands
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48
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Streptomyces morphogenetics: dissecting differentiation in a filamentous bacterium. Nat Rev Microbiol 2009; 7:36-49. [DOI: 10.1038/nrmicro1968] [Citation(s) in RCA: 465] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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